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The efforts of contrasting the effects caused by the Covid-19 (coronavirus disease 2019) pandemic increased the disposal of active pharmaceutical ingredients. This paper reports the mechanisms and kinetics of the degradation in aqueous environments induced by  OH of two drugs, among those most widely probed at the outbreak of coronavirus, nitazoxanide and hydroxychloroquine. The investigation exploits quantum chemistry techniques and a reaction rate theory combined with diffusion-controlled processes and quantum mechanical tunneling. The reaction rate constants are obtained in an environmentally relevant temperature range. The results show that (i) the deacetylation of nitazoxanide with formation of tizoxanide is kinetically the most favorable channel, in agreement with experimental work; (ii) for hydroxychloroquine, the present theoretical calculations show that the most favorable channel is the addition of  OH at the aromatic ring. The half-life time degradation products are for both cases in the range between 12 to 138 days. Both drugs presented toxicities between harmful and toxic as obtained by computational toxicology calculations: The toxicity is also calculated for the degradation products: (i) in the nitazoxanide degradation process, tizoxanide was characterized as more toxic, while (ii) in the case of hydroxychloroquine, the major degradation product showed a decrease in the toxicity.

Advances in understanding the temperature effect on water dynamics in cellular respiration are important for the modeling of integrated energy processes and metabolic rates. For more than half a century, experimental studies have contributed to the understanding of the catalytic role of water in respiration combustion, yet the detailed water dynamics remains elusive. We combine a super-Arrhenius model that links the temperature-dependent exponential growth rate of a population of plant cells to respiration, and an experiment on isotope labeled 18O2 uptake to H218O transport role and to a rate-limiting step of cellular respiration. We use Phosphofructokinase (PFK-1) as a prototype because this enzyme is known to be a pacemaker (a rate-limiting enzyme) in the glycolysis process of respiration. The characterization shows that PFK-1 water matrix dynamics are crucial for examining how respiration (PFK-1 tetramer complex breathing) rates respond to temperature change through a water and nano-channel network created by the enzyme folding surfaces, at both short and long (evolutionary) timescales. We not only reveal the nano-channel water network of PFK-1 tetramer hydration topography but also clarify how temperature drives the underlying respiration rates by mapping the channels of water diffusion with distinct dynamics in space and time. The results show that the PFK-1 assembly tetramer possesses a sustainable capacity in the regulation of the water network toward metabolic rates. The implications and limitations of the reciprocal-activation–reciprocal-temperature relationship for interpreting PFK-1 tetramer mechanisms are briefly discussed.

A molecular beam of halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) is focused by a hexapolar electrostatic field and photolyzed by UV laser radiation at 234 nm. Angular and speed distributions of chlorine and bromine photofragments emitted from halothane are measured for both spin-orbit states independently. Although the dissociation energy of the C-Cl bond is larger than that of C-Br, the relative yield of Cl to Br was found to be approximately 2. Measured speed and angular distributions of atomic fragments show distinct kinetic energy release and scattering characteristics: for bromine, observed fast and aligned fragments exhibit a signature of a direct mode of dissociation for the C-Br bond, via the electronically excited potential energy surface denoted

Numerous applications have required the study of $$\hbox {CO}_2$$ plasmas since the 1960s, from $$\hbox {CO}_2$$ lasers to spacecraft heat shields. However, in recent years, intense research activities on the subject have restarted because of environmental problems associated with $$\hbox {CO}_2$$ emissions. The present review provides a synthesis of the current state of knowledge on the physical chemistry of cold $$\hbox {CO}_2$$ plasmas. In particular, the different modeling approaches implemented to address specific aspects of $$\hbox {CO}_2$$ plasmas are presented. Throughout the paper, the importance of conducting joint experimental, theoretical and modeling studies to elucidate the complex couplings at play in $$\hbox {CO}_2$$ plasmas is emphasized. Therefore, the experimental data that are likely to bring relevant constraints to the different modeling approaches are first reviewed. Second, the calculation of some key elementary processes obtained with semi-empirical, classical and quantum methods is presented. In order to describe the electron kinetics, the latest coherent sets of cross section satisfying the constraints of “electron swarm” analyses are introduced, and the need for self-consistent calculations for determining accurate electron energy distribution function (EEDF) is evidenced. The main findings of the latest zero-dimensional (0D) global models about the complex chemistry of $$\hbox {CO}_2$$ and its dissociation products in different plasma discharges are then given, and full state-to-state (STS) models of only the vibrational-dissociation kinetics developed for studies of spacecraft shields are described. Finally, two important points for all applications using $$\hbox {CO}_2$$ containing plasma are discussed: the role of surfaces in contact with the plasma, and the need for 2D/3D models to capture the main features of complex reactor geometries including effects induced by fluid dynamics on the plasma properties. In addition to bringing together the latest advances in the description of $$\hbox {CO}_2$$ non-equilibrium plasmas, the results presented here also highlight the fundamental data that are still missing and the possible routes that still need to be investigated.

Both single-laser and two-laser experiments were conducted to look into the ion-imaging of Br*(2P1/2) and Br(2P3/2) photo-fragmented from 1-bromo-2-methylbutane in the range 232-240 nm via a detection scheme of (2+1) resonance-enhanced multiphoton ionization. The angular analysis of these photofragment distributions yields the anisotropy parameter beta = 1.88 +/- 0.06 for the Br* excited state which arises from a parallel transition, while beta = 0.63 +/- 0.09 for the Br ground state indicates the contribution from both a perpendicular transition and a non-adiabatic transition. When a hexapole coupled with an orienting field was implemented, the parent molecules are spatially oriented to yield an orientation efficiency || of 0.15. Besides the chi angle between the recoil velocity v and the transition dipole moment mu, orienting molecules allows for the evaluation of the angle alpha between v and the permanent molecular dipole moment d. The angular analysis of Br* photofragment distribution yields chi to be 11.5 degrees and alpha in the range from 160 degrees to 180 degrees with weak dependency. In the two-laser experiments, the angular anisotropy of Br photofragment distribution was found to be smaller (0.38 +/- 0.10) when the photolysis wavelength was red-shifted to 240 nm, suggesting the increasing contributions from perpendicular transitions., Comment: 36 pages, 7 figures

Molecular orientation techniques are becoming available in the study of elementary chemical processes, in order to highlight those structural and dynamical properties that would be concealed by random rotational motions. Recently successful orientation was achieved for asymmetric-top and chiral molecules of much larger complexity than hitherto. In this work, we report and discuss the correlation between the vectors' photofragment recoil velocity v, transition dipole moment μ, and permanent dipole moment d in a dissociation experiment on hexapole oriented 2-bromobutane, photoinitiated by a linearly polarized laser. The sliced ion images of the Br*(2P1/2) and Br(2P3/2) photofragments were acquired at 234.0 and 254.1 nm, respectively, by a (2 + 1) resonance-enhanced multiphoton ionization technique. A detailed analysis of the sliced ion images obtained at a tilting angle 45° of laser polarization provides information on the correlation of the three vectors, which are confined by two polar angles α and χ and one azimuthal angle φμd in the recoil frame. The sliced ion images of Br fragments eliminated individually from the enantiomers at 254.1 nm yield an asymmetric factor close to zero; for this reason the photofragment angular distributions do not show significant differences. The elimination of the Br* fragment at 234.0 nm is mainly correlated with a parallel transition, giving rise to a large anisotropy parameter of 1.85, and thus can be considered as a single state excitation. The resulting recoil frame angles are optimized to 163° ± 8° and 164° ± 1° for α and χ, respectively, whereas φμd is approaching 0° for the best fit. Since for the present molecule, the three vectors have an only slight spatial arrangement, the photofragment angular distributions of the two enantiomers do not show appreciable differences. Theoretical and computational simulations provide us the basis to state that oriented enantiomers can be discriminated on-the-fly in photodissociation processes even initiated by non-circularly polarized light, provided that the three vectors encountered above have specific three-dimensional arrangements. The fact that Br fragment elimination involves a multi-potential dissociation carries uncertainties in theoretical estimates of the vector direction. Therefore, this work represents a preliminary but significant step on the road to chiral discrimination on-the-fly, which is shown to be best propitiated in molecules where vectors are far from having degenerate mutual angular directions.

The representation of the potential energy surfaces of atom molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic molecule diatomic molecule interactions are shown., 4 pages, 2 figures

A variety of current experiments and molecular dynamics computations are expanding our understanding of rate processes occurring in extreme environments, especially at low temperatures, where deviations from linearity of Arrhenius plots are revealed. The thermodynamic behavior of molecular systems is determined at a specific temperature within conditions on large volume and number of particles at a given density (the thermodynamic limit): on the other side, kinetic features are intuitively perceived as defined in a range between the extreme temperatures, which limit the existence of each specific phase. In this paper, extending the statistical mechanics approach due to Fowler and collaborators, ensembles and partition functions are defined to evaluate initial state averages and activation energies involved in the kinetics of rate processes. A key step is delayed access to the thermodynamic limit when conditions on a large volume and number of particles are not fulfilled: the involved mathematical analysis requires consideration of the role of the succession for the exponential function due to Euler, precursor to the Poisson and Boltzmann classical distributions, recently discussed. Arguments are presented to demonstrate that a universal feature emerges: Convex Arrhenius plots (super-Arrhenius behavior) as temperature decreases are amply documented in progressively wider contexts, such as viscosity and glass transitions, biological processes, enzymatic catalysis, plasma catalysis, geochemical fluidity, and chemical reactions involving collective phenomena. The treatment expands the classical Tolman&rsquo, s theorem formulated quantally by Fowler and Guggenheim: the activation energy of processes is related to the averages of microscopic energies. We previously introduced the concept of &ldquo, transitivity&rdquo, a function that compactly accounts for the development of heuristic formulas and suggests the search for universal behavior. The velocity distribution function far from the thermodynamic limit is illustrated, the fraction of molecules with energy in excess of a certain threshold for the description of the kinetics of low-temperature transitions and of non-equilibrium reaction rates is derived. Uniform extension beyond the classical case to include quantum tunneling (leading to the concavity of plots, sub-Arrhenius behavior) and to Fermi and Bose statistics has been considered elsewhere. A companion paper presents a computational code permitting applications to a variety of phenomena and provides further examples.

A survey on the principles of chemical kinetics (the “science of change”) is presented here. This discipline plays a key role in molecular sciences, however, the debate on its foundations had been open for the 130 years since the Arrhenius equation was formulated on admittedly purely empirical grounds. The great success that this equation has had in the development of experimental research has motivated the need of clarifying its relationships with the foundations of thermodynamics on the one hand and especially with those of statistical mechanics (the “discipline of chances”) on the other. The advent of quantum mechanics in the Twenties and the scattering experiments by molecular beams in the second half of last century have validated collisional mechanisms for reactive processes, probing images of single microscopic events; molecular dynamics computational techniques have been successfully applied to interpret and predict phenomena occurring in a variety of environments: the focus here is on a key aspect, the effect of temperature on chemical reaction rates, which in cold environments show departure from Arrhenius law, so arguably from Maxwell–Boltzmann statistics. Modern developments use venerable mathematical concepts arising from “criteria for choices” dating back to Jacob Bernoulli and Euler. A formulation of recent progress is detailed in Aquilanti et al. 2017.

The spherical-harmonics expansion is a mathematically rigorous procedure and a powerful tool for the representation of potential energy surfaces of interacting molecular systems, determining their spectroscopic and dynamical properties, specifically in van der Waals clusters, with applications also to classical and quantum molecular dynamics simulations. The technique consists in the construction (by ab initio or semiempirical methods) of the expanded potential interaction up to terms that provide the generation of a number of leading configurations sufficient to account for faithful geometrical representations. This paper reports the full general description of the method of the spherical-harmonics expansion as applied to diatomic-molecule-diatomic-molecule systems of increasing complexity: the presentation of the mathematical background is given for providing both the application to the prototypical cases considered previously (O2-O2, N2-N2, and N2-O2 systems) and the generalization to: (i) the CO-CO system, where a characteristic feature is the lower symmetry order with respect to the cases studied before, requiring a larger number of expansion terms necessary to adequately represent the potential energy surface; and (ii) the CO-HF system, which exhibits the lowest order of symmetry among this class of aggregates and therefore the highest number of leading configurations., 13 figures, 5 tables, special issue in honor of Walther Caminati

This paper reports a study of the quantum reaction dynamics and kinetics of the F + HD reaction at low and ultralow temperatures, focusing on the range from the Wigner limit up to 50 K. Close coupling time-independent quantum reactive scattering calculations for the production of HF and DF molecules have been carried out on two potential energy surfaces differing in the description of the reaction entrance channel. This case is computationally more demanding than the cases of F with H-2 and D-2 (De Fazio et al. Frontiers in Chemistry, 2019, 7, 328) but offers a wider phenomenology regarding the roles of quantum mechanical effects of tunneling, of virtual states, and of resonances. The results show that at the temperatures in the cold and ultracold regimes small changes in the entrance channel long-range interaction induce surprising near threshold features. The presence of a virtual state close to the reactive threshold gives rise to a marked anti-Arrhenius behavior of the rate constants below 100 mK. This effect enhances reaction rates by about 2 orders of magnitude, making them of the same order as those at room temperature and confining the onset of the Wigner regime in the microkelvin region.

Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic sampling of the canonical ensemble is indicated as needed for quantitative comparison with the kinetic experiments.

For the prototypical diatomic-molecule - diatomic molecule interactions H2-HX and H2-X2, where X = F, Cl, Br, quantum-chemical ab initio calculations are carried out on grids of the configuration space, which permit a spherical-harmonics representation of the potential energy surfaces (PESs). Dimer geometries are considered for sets of representative leading configurations, and the PESs are analyzed in terms of isotropic and anisotropic contributions. The leading configurations are individuated by selecting a minimal set of mutual orientations of molecules needed to build the spherical-harmonic expansion on geometrical and symmetry grounds. The terms of the PESs corresponding to repulsive and bonding dimer geometries and the averaged isotropic term, for each pair of interacting molecules, are compared with representations in terms of a potential function proposed by Pirani et al. (see Chem. Phys. Lett. 2004, 394, 37-44 and references therein). Connections of the involved parameters with molecular properties provide insight into the nature of the interactions., 27 pages, 8 figures, 4 tables

Alternative to conventional structural diagrams that plot dihedral angles of aminoacids in the protein chains, the proposed screen representation is based on significant distances in the aminoacid unit. Here, we report the case of alanine, the simplest chiral aminoacid, both isolated and participating in about fifty peptidic chains, of length included between 43 and 2238 aminoacid units. We present comparison with the most stable conformer in the isolated form (NH2-CH-CH3-COOH), in order to find possible effects in bond lengths due to aminoacid substituents. We have also found that serine is the aminoacid most frequently connected to alanine. Screen points of alanine, when bounded to serine, are displayed and highlighted in order to evidence how this aminoacid, exemplary for the substituent groups, affects the alanine structure.Alternative to conventional structural diagrams that plot dihedral angles of aminoacids in the protein chains, the proposed screen representation is based on significant distances in the aminoacid unit. Here, we report the case of alanine, the simplest chiral aminoacid, both isolated and participating in about fifty peptidic chains, of length included between 43 and 2238 aminoacid units. We present comparison with the most stable conformer in the isolated form (NH2-CH-CH3-COOH), in order to find possible effects in bond lengths due to aminoacid substituents. We have also found that serine is the aminoacid most frequently connected to alanine. Screen points of alanine, when bounded to serine, are displayed and highlighted in order to evidence how this aminoacid, exemplary for the substituent groups, affects the alanine structure.

In this survey we account for basic mathematical ingredients for dealing with quantum chemical problems. We focus on comprehensive previous work (Coletti et al., 2013, pp. 74–127, Ref. 1 ) documenting relationships with the Askey scheme, a classification of the orthogonal polynomials sets of hypergeometric type. A reduction of the scheme is proposed individuating nine fundamental functional sets which have their counterparts in quantum mechanics; they occur in the general Kepler–Coulomb problem: as well known basis sets for expansions of orbitals in quantum chemistry and in the treatment of specific atomic and molecular applications. A novelty of the approach, with respect to this extensively covered topic, is the establishment of this representation for Kravchuk polynomials, on the mathematical side and, correspondingly, of the spherical top wavefunctions on the physical side: the latter are explicitly connected with the Wigner's rotation matrix of angular momentum theory. Novel presentations of the Askey-type hierarchy of hypergeometrical orthonormal basis sets relevant in quantum mechanics and the relationships connecting them are established by powerful tools: from the mathematical viewpoint, the Askey duality and asymptotic analysis; from a physical viewpoint, the symmetry by transposition and semiclassical limits. A new three-by-three matrix visualization illustrates the set of correspondences to assist further work on the path connecting classical and quantum physics and discrete and continuous mathematics that is presented elsewhere (Coletti et al., 2019, Ref. 46 ). This is pictured as a bridge where Racah polynomials and harmonic oscillator wavefunctions are the corner stones, while the rotation matrix of Wigner is the keystone. Here, the path is illustrated as the steps of a stairway that we define as the Jacobi ladder, where going up and down is insightful for applications. Extension to the full Askey scheme, object of future work, is briefly noted: some reference is made to our recent progress in spherical to hyperspherical manifold representations involving the q-scheme of Askey and related orthogonal polynomials as possible orthonormal basis sets in quantum mechanics.

The hyperspherical coordinate systems have been extensively adopted in the study of few-body scattering problems of nuclear and molecular physics, for example in the practical implementation of demanding quantum calculations typical of chemical reactions. Hyperangular momenta are the dynamical quantities used in this representation and the hyperspherical harmonics are the corresponding basis functions. The use of such formalism is limited to the treatment of three- or four-center problems, due to the exceedingly high computational cost of quantum dynamics calculations. To circumvent this restriction, an hyperspherical formulation has been developed in a series of works during the last decades, suitable for the simulation of cluster and large molecular system dynamics. Such a hyperspherical formulation is based on classical definitions of the hyperangular momenta and on the search of invariant dynamical quantities. Exploiting invariance of hyperspherical shape coordinates with respect to rotations and kinematic rotations, we consider the use of the classical hyperspherical representation as a tool for the static analysis of geometry and minimum energy structures of atomic and molecular structures, showing some applications to relatively simple systems.